Casey Stella's document discusses the integration of natural language processing (NLP) techniques, particularly word2vec, into the analysis of structured clinical data. By conceptualizing clinical encounters as sentences, the document explores leveraging unsupervised machine learning to uncover relationships within medical data. It highlights challenges faced by data scientists in merging analytical skills with domain expertise and presents a demo involving the preprocessing of clinical records into a dataset for further analysis.

1. NLP Structured Data Investigation on Non-Text
Casey Stella
April, 2015
Casey Stella (Hortonworks) NLP Structured Data Investigation on Non-Text April, 2015

2. Table of Contents
Preliminaries
Borrowing from NLP
Demo
Questions
Casey Stella (Hortonworks) NLP Structured Data Investigation on Non-Text April, 2015

3. Introduction
• I’m a Principal Architect at Hortonworks
• I work primarily doing Data Science in the Hadoop Ecosystem
• Prior to this, I’ve spent my time and had a lot of fun
◦ Doing data mining on medical data at Explorys using the Hadoop
ecosystem
◦ Doing signal processing on seismic data at Ion Geophysical using
MapReduce
◦ Being a graduate student in the Math department at Texas A&M in
algorithmic complexity theory
Casey Stella (Hortonworks) NLP Structured Data Investigation on Non-Text April, 2015

4. Domain Challenges in Data Science
A data scientist has to merge analytical skills with domain expertise.
• Often we’re thrown into places where we have insufficient domain
experience.
• Gaining this expertise can be challenging and time-consuming.
• Unsupervised machine learning techniques can be very useful to
understand complex data relationships
Casey Stella (Hortonworks) NLP Structured Data Investigation on Non-Text April, 2015

5. Domain Challenges in Data Science
A data scientist has to merge analytical skills with domain expertise.
• Often we’re thrown into places where we have insufficient domain
experience.
• Gaining this expertise can be challenging and time-consuming.
• Unsupervised machine learning techniques can be very useful to
understand complex data relationships
We’ll use an unsupervised structure learning algorithm borrowed from
NLP to look at medical data.
Casey Stella (Hortonworks) NLP Structured Data Investigation on Non-Text April, 2015

6. Word2Vec
Word2Vec is a vectorization model created by Google [1] that
attempts to learn relationships between words automatically given a
large corpus of sentences.
• Gives us a way to find similar words by finding near neighbors in the
vector space with cosine similarity.
1
http://radimrehurek.com/2014/12/making-sense-of-word2vec/
Casey Stella (Hortonworks) NLP Structured Data Investigation on Non-Text April, 2015

7. Word2Vec
Word2Vec is a vectorization model created by Google [1] that
attempts to learn relationships between words automatically given a
large corpus of sentences.
• Gives us a way to find similar words by finding near neighbors in the
vector space with cosine similarity.
• Uses a neural network to learn vector representations.
1
http://radimrehurek.com/2014/12/making-sense-of-word2vec/
Casey Stella (Hortonworks) NLP Structured Data Investigation on Non-Text April, 2015

8. Word2Vec
Word2Vec is a vectorization model created by Google [1] that
attempts to learn relationships between words automatically given a
large corpus of sentences.
• Gives us a way to find similar words by finding near neighbors in the
vector space with cosine similarity.
• Uses a neural network to learn vector representations.
• Recent work by Pennington, Socher, and Manning [2] shows that
the word2vec model is equivalent to weighting a word co-occurance
matrix weighting based on window distance and lowering the
dimension by matrix factorization.
1
http://radimrehurek.com/2014/12/making-sense-of-word2vec/
Casey Stella (Hortonworks) NLP Structured Data Investigation on Non-Text April, 2015

9. Word2Vec
Word2Vec is a vectorization model created by Google [1] that
attempts to learn relationships between words automatically given a
large corpus of sentences.
• Gives us a way to find similar words by finding near neighbors in the
vector space with cosine similarity.
• Uses a neural network to learn vector representations.
• Recent work by Pennington, Socher, and Manning [2] shows that
the word2vec model is equivalent to weighting a word co-occurance
matrix weighting based on window distance and lowering the
dimension by matrix factorization.
Takeaway: The technique boils down, intuitively, to a riff on word
co-occurence. See here1 for more.
1
http://radimrehurek.com/2014/12/making-sense-of-word2vec/
Casey Stella (Hortonworks) NLP Structured Data Investigation on Non-Text April, 2015

10. Clinical Data as Sentences
Clinical encounters form a sort of sentence over time. For a given
encounter:
• Vitals are measured (e.g. height, weight, BMI).
• Labs are performed and results are recorded (e.g. blood tests).
• Procedures are performed.
• Diagnoses are made (e.g. Diabetes).
• Drugs are prescribed.
Each of these can be considered clinical “words” and the encounter
forms a clinical “sentence”.
Casey Stella (Hortonworks) NLP Structured Data Investigation on Non-Text April, 2015

11. Clinical Data as Sentences
Clinical encounters form a sort of sentence over time. For a given
encounter:
• Vitals are measured (e.g. height, weight, BMI).
• Labs are performed and results are recorded (e.g. blood tests).
• Procedures are performed.
• Diagnoses are made (e.g. Diabetes).
• Drugs are prescribed.
Each of these can be considered clinical “words” and the encounter
forms a clinical “sentence”.
Idea: We can use word2vec to investigate connections between these
clinical concepts.
Casey Stella (Hortonworks) NLP Structured Data Investigation on Non-Text April, 2015

12. Demo
As part of a Kaggle competition2, Practice Fusion, a digital electronic
medical records provider released depersonalized clinical records of
10,000 patients. I ingested and preprocessed these records into
197,340 clinical “sentences” using Pig and Hive.
2
https://www.kaggle.com/c/pf2012-diabetes
Casey Stella (Hortonworks) NLP Structured Data Investigation on Non-Text April, 2015

13. Demo
As part of a Kaggle competition2, Practice Fusion, a digital electronic
medical records provider released depersonalized clinical records of
10,000 patients. I ingested and preprocessed these records into
197,340 clinical “sentences” using Pig and Hive.
MLLib from Spark now contains an implementation of word2vec, so
let’s use pyspark and IPython Notebook to explore this dataset on
Hadoop.
2
https://www.kaggle.com/c/pf2012-diabetes
Casey Stella (Hortonworks) NLP Structured Data Investigation on Non-Text April, 2015

14. Questions
Thanks for your attention! Questions?
• Code & scripts for this talk available on my github presentation
page.3
• Find me at http://caseystella.com
• Twitter handle: @casey_stella
• Email address: cstella@hortonworks.com
3
http://github.com/cestella/presentations/
Casey Stella (Hortonworks) NLP Structured Data Investigation on Non-Text April, 2015

15. Bibliography
[1] Tomas Mikolov, Kai Chen, Greg Corrado, and Jeffrey Dean.
Efficient estimation of word representations in vector space. CoRR,
abs/1301.3781, 2013.
[2] Jeffrey Pennington, Richard Socher, and Christopher Manning.
Glove: Global vectors for word representation. In Proceedings of
the 2014 Conference on Empirical Methods in Natural Language
Processing (EMNLP), pages 1532–1543. Association for
Computational Linguistics, 2014.
Casey Stella (Hortonworks) NLP Structured Data Investigation on Non-Text April, 2015